Contacts of the helix formed by residues 70 - 81 (chain A) in PDB entry 5K58
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ILE* 3.2 37.7 + - + +
67A GLU 4.2 5.4 - - - +
69A SER* 1.3 79.5 - - - +
71A ILE* 1.3 83.6 + - + +
73A ARG 3.5 0.3 + - - -
74A ILE* 3.0 35.9 + - + +
94A LEU* 3.3 14.9 - - + +
95A LEU* 3.9 20.4 - - + -
98A PHE* 5.7 3.3 - - + -
109A LEU* 5.7 2.7 - - + -
128A LEU* 3.6 20.2 - - + +
131A ARG* 4.8 4.3 - - + +
132A ILE* 3.6 38.8 - - + +
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU 3.0 24.5 - - - +
68A ASP* 3.7 8.1 - - - +
70A LEU* 1.3 83.3 - - + +
72A THR* 1.3 67.6 + - - +
74A ILE* 2.9 24.7 + - + +
75A ASN* 2.9 39.0 + - - +
131A ARG* 3.6 27.8 - - + +
132A ILE* 5.9 0.9 - - - +
135A GLN* 3.7 30.3 - - + +
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASP* 2.8 42.8 + - - +
69A SER* 5.2 0.9 - - - -
71A ILE* 1.3 75.8 - - - +
73A ARG* 1.3 61.6 + - + +
74A ILE 3.3 0.9 + - - -
75A ASN* 3.7 12.1 + - + +
76A LEU* 3.5 19.4 + - - +
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A SER* 3.1 24.9 + - - +
70A LEU 3.5 1.2 + - - -
71A ILE 3.2 0.6 - - - -
72A THR* 1.3 79.9 - - + +
74A ILE* 1.3 59.4 + - - +
76A LEU* 3.6 32.4 - - - +
77A ILE* 3.0 24.3 + - - +
94A LEU* 3.8 22.8 - - + +
372L LEU* 3.6 16.3 - - - +
373L ASP* 3.2 56.1 + - - +
375L PRO* 4.8 9.4 - - + +
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.0 26.6 + - + +
71A ILE* 2.9 14.6 + - + +
73A ARG* 1.3 76.6 - - - +
75A ASN* 1.3 60.5 + - - +
76A LEU 3.0 1.6 - - - -
77A ILE* 2.7 26.3 + - + +
78A LEU* 3.0 16.1 + - + +
91A ILE* 3.8 48.7 - - + -
94A LEU* 3.5 16.8 - - + -
95A LEU* 5.8 1.6 - - + -
132A ILE* 4.7 20.9 - - + +
135A GLN* 3.9 26.2 - - + +
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 2.9 46.4 + - - +
72A THR* 4.0 10.5 - - - +
74A ILE* 1.3 75.1 - - - +
76A LEU* 1.3 61.4 + - - +
78A LEU* 3.4 14.4 + - + +
79A LYS* 3.3 22.5 + - - +
135A GLN* 3.7 10.9 + - - -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR 3.5 10.5 + - - +
73A ARG* 3.6 45.1 - - - +
74A ILE 3.0 0.2 - - - -
75A ASN* 1.3 77.0 - - - +
77A ILE* 1.3 64.4 + - + +
79A LYS* 3.1 30.8 - - + +
80A ASP* 2.7 36.6 - - - +
372L LEU* 4.8 8.1 - - + -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG 3.0 21.3 - - - +
74A ILE* 2.7 20.9 + - + +
76A LEU* 1.3 71.3 - - - +
78A LEU* 1.3 63.8 + - + +
79A LYS 3.0 1.4 + - - -
80A ASP* 3.0 16.1 + - - +
81A GLU* 3.2 15.2 + - + +
87A ARG* 3.7 22.7 - - + +
90A LEU* 3.6 40.1 - - + +
91A ILE* 3.6 35.9 - - + +
94A LEU* 4.4 5.8 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.0 20.4 + - + +
75A ASN* 3.6 21.8 - - - +
77A ILE* 1.3 74.6 - - - +
79A LYS* 1.3 56.8 + - - +
81A GLU 3.4 0.5 - - - +
82A LYS* 3.1 16.4 + - - +
87A ARG* 2.6 54.6 + - + +
91A ILE* 4.5 3.6 - - + -
135A GLN* 3.3 29.8 - - + +
139A VAL* 4.1 18.6 - - + -
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASN 3.3 8.4 + - - +
76A LEU* 3.1 37.4 + - + +
77A ILE 3.1 1.2 - - - -
78A LEU* 1.3 78.8 - - - +
80A ASP* 1.3 69.3 + - - +
81A GLU 3.7 0.2 - - - -
82A LYS* 3.3 25.2 + - - +
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 2.7 40.4 - - - +
77A ILE* 3.0 6.1 + - - +
79A LYS* 1.3 91.7 - - - +
81A GLU* 1.3 60.9 + - + +
82A LYS* 5.4 0.7 - - - -
90A LEU* 6.5 1.1 - - + -
372L LEU* 4.5 13.7 - - + +
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE 3.2 8.2 + - - +
78A LEU 3.4 0.6 - - - +
80A ASP* 1.3 78.1 - - + +
82A LYS* 1.3 80.6 + - - +
83A ASP* 2.7 30.2 + - - +
86A ALA* 3.6 27.6 - - + +
87A ARG* 3.1 29.8 + - - +
90A LEU* 5.0 12.3 - - + -
146A ARG* 4.9 4.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il